I would like to map short reads against a reference database for viral discovery using bowtie2. However, since I don't know what I'm looking for, I need a way to parse the output to filter out spurious hits and focus on more interesting things. I was hoping there was a way to format a sam/bam file similar to the tabular output using Blast. Or at least a way to get a list of headers from the bowtie2 index and correlating sequences/mapQ scores from my data. Any suggestions? Thanks! And FYI, I was originally Blasting my sequences but it was prohibitively slow.